Centre for Animal Science - Winter Research Programs 2026 Projects

Primary Supervisor: A/Prof Elizabeth Ross | e.ross@uq.edu.au

Please contact A/Prof Elizabeth Ross (e.ross@uq.edu.au) prior to submitting your application for this project. Ensure that you include a copy of your CV and academic transcript as attachments to your email.

Duration: 4 weeks (30 hours per week); onsite

Location: UQ St Lucia Campus

Strawberry (Fragaria × ananassa) has a large, highly repetitive, polyploid genome, which makes it a perfect “real genomics” challenge: standard short-read approaches often miss the big changes, but long reads let you see them directly. You’ll use existing nanopore datasets to discover, curate, and interpret large SVs (insertions, deletions, inversions, duplications, translocations) and then connect them to biology: genes, regulatory regions, and trait-relevant loci (e.g., flavour/aroma, firmness/shelf-life, flowering time, and disease resistance).

Expected outcomes: Students will gain practical experience calling and curating structural variants (SVs) from long-read nanopore data (the “hard stuff” many teams outsource). Students will develope confidence working with complex, repetitive, polyploid plant genomes.

Suitability: This project is open to applications from undergraduate or masters students with bioinformatics or computational biology experience. 

Primary Supervisor: A/Prof Elizabeth Ross | e.ross@uq.edu.au

Please contact A/Prof Elizabeth Ross (e.ross@uq.edu.au) prior to submitting your application for this project. Ensure that you include a copy of your CV and academic transcript as attachments to your email.

Duration: 4 weeks (30 hours per week); onsite

Location: UQ St Lucia Campus

This project builds on genotyping-by-sequencing methods where low-coverage long-read data from Oxford Nanopore Technologies has been shown to produce genotypes (and downstream genomic predictions) that closely match SNP-array benchmarks. 
Your job is to turn existing nanopore datasets into a robust, species-agnostic genotyping pipeline: align reads, call genotype likelihoods, impute dense SNP panels using reference haplotypes, and produce clear summary outputs (PCA/relatedness, call-rate vs accuracy curves, per-species QC dashboards, and a final curated genotype resource). The project is deliberately cross-species: you’ll learn how to adapt the same core workflow to different genome sizes, reference quality, and available panels—exactly the kind of applied genomics skillset that transfers to biotech, breeding, conservation genomics, and research.

Expected outcomes: Students will gain practical experience performing genotyiing from long-read nanopore data . Students will develope confidence working with long read sequence data and developing applied pipelines.

Suitability: This project is open to applications from undergraduate or masters students with bioinformatics or computational biology experience. 

Primary Supervisor: Dr Loan Nguyen | t.nguyen3@uq.edu.au

Please contact Dr Loan Nguyen (t.nguyen3@uq.edu.au) prior to submitting your application for this project. Ensure that you include a copy of your CV and academic transcript as attachments to your email.

Duration: 4 weeks (30 hours per week); On-site

Location: UQ St Lucia Campus

This project will use Pore-C Oxford Nanopore sequencing to profile pre- and post-pubertal heifers. The student will perform cross-linking, DNA extraction, library preparation, and sequencing using a PromethION P2 device. Strong molecular laboratory skills—including high-quality DNA extraction and quality control (QC)—are required.

Expected outcomes: Through this project, the student will gain hands-on experience with third-generation sequencing and associated wet-lab workflows, which will be highly valuable for future research and industry applications.

Suitability:  This project is open to applications from undergraduate or master students with strong molecular skills. 

Primary Supervisor: 

Dr Natasha Hungerford | n.hungerford@uq.edu.au
Dr Viviene Santiago | v.santiago@uq.edu.au
Dr Isobella Stone | i.stone@uq.edu.au

Please contact Dr Natasha Hungerford (n.hungerford@uq.edu.au) or Dr Viviene Santiago (v.santiago@uq.edu.au) or Dr Isobella Stone (i.stone@uq.edu.au) before applying

Duration: 4 weeks (30 hours per week); on site 

Location: Health and Food Sciences Precinct, 39 Kessels Rd, Coopers Plains

This project focuses on the isolation, identification and analysis of the hepatotoxic amino acid indospicine in Indigofera leaf samples. Indospicine, an unusual analogue of arginine found in all parts of certain Indigofera species, is known to be hepatotoxic and has been linked to toxicity in domestic dogs in Australia from contaminated horse and camel meat in pet food. Prolonged ingestion of indospicine has been reported to result to mild to severe liver disease. However, recent studies have also shown that indospicine can replace arginine and improve outcomes of enzymatic arginine deprivation (ADT), a metabolic anticancer therapy currently being evaluated in clinical trials. This project will examine the indospicine content of leaf samples using LC-MS/MS and HPLC-PDA analysis and examine isolation of indospicine from these samples.

Expected outcomes: Scholars will gain skills in the use of HPLC, LC-MS/MS analysis and isolation techniques and will generate research data that is expected to lead to a publication.

Suitability: This project is open to applications from students with a background in organic chemistry with an interest in analytical chemistry. 

Primary Supervisor: Dr Lida Omaleki | l.omaleki@uq.edu.au

Please contact Contact Dr Lida Omaleki (l.omaleki@uq.edu.au) prior to submitting your application for this project.

Duration: 4 weeks (30 - 36 hours per week); On-site

Location: Ecosciences Precinct, Dutton Park

Pasteurella multocida is a multi‑host pathogen responsible for significant disease in numerous agriculturally important animals and wildlife species. This project aims to optimise RNA extraction from this organism to ensure high‑quality, intact RNA suitable for downstream molecular applications. In particular, the optimised extraction protocol will be used to perform quantitative PCR (qPCR) targeting sugar transferase genes involved in the biosynthesis of the outer lipopolysaccharide (LPS) layer. Improving RNA yield and purity will enable accurate quantification of these genes and support a deeper understanding of LPS assembly and virulence‑associated pathways in P. multocida.

Expected outcomes: The person will develop practical skills in laboratory methods inclusing RNA extraction and qPCR analysis. 

Suitability:  This project is open to applications from  undergraduate or masters students with microbiology and/or molecular biology experience.

Primary Supervisors: 

Dr Chensong Chen  | chensong.chen@uq.edu.au
Dr Eric Dinglasan | e.dinglasan@uq.edu.au

Please contact Dr Chensong Chen (chensong.chen@uq.edu.au) and Dr Eric Dinglasan (e.dinglasan@uq.edu.au) before submitting an application.

Duration: 4 weeks (20-30 hours per week); on site

Location: UQ St Lucia Campus

Modern crop breeding programs require predictive models capable of fully capturing genetic merit. Deep and graph‑based architectures can model epistasis, gene‑network regulation, and environment‑dependent effects that underlie complex agronomic traits. Integrating multi‑omics data into these models further improves prediction accuracy for yield, stress tolerance, and quality traits, thereby accelerating genomic selection and crop‑improvement pipelines.

Expected outcomes: The scholar will gain experiences of developing bioinformatic pipelines, basic skills of existing AI frameworks (sklearn, Torch, Tensorflow) and concept of genomic selection.

Suitability: This project is open to applications from 3 or 4 year Undergraduate or master students with a background of geneics/genomics/crop science. Suitable for students with a previous programming experience.

Primary Supervisors: 

Dr Hannah Siddle  | h.siddle@uq.edu.au
Prof. Ala Tabor  | a.tabor@uq.edu.au

Please contact Dr Hannah Siddle (h.siddle@uq.edu.au) or Prof. Ala Tabor (a.tabor@uq.edu.au) for further information.

Duration: 4 weeks (30 hours per week); on site

Location: UQ St Lucia Campus

The cattle tick is a major burden on Australia’s multibillion dollar beef industry and global food security. The only treatments are chemicals called acaricides, but ticks are rapidly developing resistance, severely reducing control options. In this project, the student will use novel rapid testing kits to test ticks for resistance to chemicals. Ticks with reistsant phenotypes will be targeted for long read genome sequencing to define markers of resistance. 

Expected outcomes: This winter project can involve both field work and/or laboratory work, depending on the students preference. The fieldwork will involve collecting ticks from cattle in the field, under direct supervision. Laboratory work will give the student hands on experience in DNA extraction and long read genome sequencing.

Suitability: The project is suitable for students with an interest in parisitology, molecular biolgy and/or genomics.